import scanpy as sc, anndata as ad, numpy as np, pandas as pd
from scipy import sparse
from anndata import AnnData
import warnings
import socket
import holoviews as hv
import plotly.express as px
import random
import itertools
from matplotlib import pylab
import sys
import yaml
import os
from pandas.api.types import CategoricalDtype
import plotly
import scvelo as scv
random.seed(0)
import matplotlib.pyplot as plt
warnings.filterwarnings('ignore')
plotly.offline.init_notebook_mode()
import anndata2ri
import rpy2.rinterface_lib.callbacks
import logging
import ipynbname
try:
nb_fname = ipynbname.name()
except:
nb_fname = "".join(os.path.basename(globals()["__vsc_ipynb_file__"]).split(".")[:-1])
rpy2.rinterface_lib.callbacks.logger.setLevel(logging.ERROR)
anndata2ri.activate()
%load_ext rpy2.ipython
%%R
library(miloR)
library(igraph)
set.seed(0)
%matplotlib inline
sc.settings.verbosity = 3 # verbosity: errors (0), warnings (1), info (2), hints (3)
sc.logging.print_header()
sc.settings.set_figure_params(dpi=50, facecolor='white', dpi_save=500)
pylab.rcParams['figure.figsize'] = (9, 9)
outBaseName = "04.1A_Neurons_DA"
figDir = "./figures"
scanpy==1.8.1 anndata==0.7.6 umap==0.4.6 numpy==1.20.2 scipy==1.6.3 pandas==1.2.4 scikit-learn==0.24.2 statsmodels==0.13.1 python-igraph==0.9.8 louvain==0.7.1 pynndescent==0.5.5
hostRoot = "-".join(socket.gethostname().split('-')[0:2])
#indir=paths["paths"]["indir"][hostRoot]
outdir="./outdir"
leiden3Mapping = {"0":"Encs-1",
"1":"CBC/BRCs-1",
"2":"EXN-1",
"3":"EnCs-2",
"4":"RGCs-1",
"5":"RGCs-2",
"6":"ccRGCs",
"7":"inPCs",
"8":"EXN-2",
"9":"RtCs",
"10":"ER-Cs",
"11":"CBC/BRCs-2"}
adata = sc.read_h5ad(outdir+"/3_polaroid_quickAnno.h5ad")
adata.obs["leidenAnno"] = adata.obs["leiden0.3"].replace(leiden3Mapping).astype("category").cat.reorder_categories(list(leiden3Mapping.values()))
adata.uns["leidenAnno_colors"] = adata.uns["leiden0.3_colors"].copy()
pylab.rcParams['figure.figsize'] = (9, 9)
sc.pl.umap(adata, color=["organoid","type","dataset","leidenAnno","MKI67"],
ncols = 2, size = 30, add_outline = True,
outline_width=(0.2, 0.05), frameon=False, wspace=.5)